• Journal of Veterinary Science
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• v.21 no.1
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• pp.11.1-11.7
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• 2020

The increase in canine skin and soft tissue infections, such as pyoderma and otitis, caused by Staphylococcus schleiferi strains, is of significant zoonotic concern. In this study, we report the first complete genome sequence for a methicillin-resistant clinical isolate of S. schleiferi (MRSS) designated as SS4, obtained from a dog with otitis externa, in Korea. The genome of SS4 strain was of 2,539,409 bp and presented high G+C content ratio (35.90%) with no plasmid. Comparative analysis of SS4 genome revealed that it is closely related to 2142-05 and 5909-02 strains isolated from the canine skin infections in the USA.

• Korean Journal of Microbiology
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• v.54 no.1
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• pp.74-76
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• 2018

Recently, Fusobacterium nucleatum subsp. vincentii was reclassified as Fusobacterium vincentii based on the average nucleotide identity and genome-to-genome distance analyses. F. vincentii is a Gram-negative, anaerobic, and filament-shaped bacterium. F. vincentii is a member of normal flora of human oral cavity and plays a role in periodontal diseases. F. vincentii KCOM 2931 was isolated from a periodontitis lesion. Here, we present the complete genome sequence of F. vincentii KCOM 2931.

• Korean Journal of Microbiology
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• v.53 no.4
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• pp.326-328
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• 2017

Herbaspirillum sp. meg3 belonging to Betaproteobacteria was isolated from soil in Jeju island. Here, we report the complete genome sequence of strain meg3 with a size of approximately 5.47 Mb and a mean G + C content of 57.1%. The genome included 4,816 coding sequences, and 9 ribosomal RNA and 51 transfer RNA genes. In the genome, two incomplete prophage regions have been identified. Also, we propose that strain meg3 has a potential capability for aromatic-compounds degradation based on the result of genome analysis.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 2003.10a
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• pp.113.1-113
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• 2003

A potexvirus, Hosta virus X (HVX-Kr), causing mosaic and mottle symptoms was isolated from hosta plants (Hosta spp.), and its entire genome RNA sequence was determined. in Korea using cDNA library and RACE methods. The genome of HVX encodes five open reading frames coding for viral replicase, triple gene block (TGB), and viral coat protein (CP) from the 5'to 3' ends, which is a typical genome structure of potexviruses. The 3-terminal region of the virus includes the TGBI (26 kDa), TGB2 (13 kDa), TGB3 (8 kDa), and 23 kDa coat protein (CP) and the 3-nontranslated region (NTR). The CP gene of the type isolate of HVX (HVX-U) was amplified by RT-PCR and its nucleotide sequence was determined. The CPs of HVX-Kr and HVX-U had 100％ and 98.9％ identical amino acids and nucleotides, respectively. Most of the regions of the genome HVX had over 50％ nucleotide identical to other sequenced potexviruses. This is the first report of complete genome sequence information of HVX and molecular evidence supporting the virus as a distinct species of the genus Potexvirus.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 2003.10a
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• pp.147.2-148
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• 2003

Complete nucleotide sequence of genome RNA of a Korean isolate of Pepper mottle virus (PepMoV-Vb) from field-collected diseased paprika (Capsicum annuum var grossum) was determined in this study. Symptoms of isolates of PepMoV were divided largely into two groups, vein banding (Vb) and vein clearing (Vc) patterns. PepMoV-Vb RNA consists of 9,640 nucleotides excluding the poly(A) tail. A single open reading frame was identified beginning at nucleotide position 169 encoding a polyprotein of 3024 amino acids which is typical of the Potyvirus genus. The complete nucleotide sequence and coding regions of PepMoV-Vb were compared to that of 11 potyviruses within the genus Potyvirus. The overall nucleotide sequence identity was 94.7 and 94.1％ identical to PepMoV-C and PepMoV-FL, respectively. Full-length cDNAs of PepMoV-Vbl were synthesized from purified viral RNAs by RT-PCR and their genome structure was analysed by RFLP analysis. This is the first report on complete nucleotide sequence of PepMoV isolated from paprika in Korea.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.56-58
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• 2000

Post-genomics may be defined in different ways depending on how one views the challenges after the genome. A popular view is to follow the concept of the central dogma in molecular biology, namely from genome to transcriptome to proteome. Projects are going on to analyze gene expression profiles both at the mRNA and protein levels and to catalog protein 3D structure families, which will no doubt help the understanding of information in the genome. However complete, such catalogs of genes, RNAs, and proteins only tell us about the building blocks of life. They do not tell us much about the wiring (interaction) of building blocks, which is essential for uncovering systemic functional behaviors of the cell or the organism. Thus, an alternative view of post-genomics is to go up from the molecular level to the cellular level, and to understand, what I call, the "interactome"or a complete picture of molecular interactions in the cell. KEGG (http://www.genome.ad.jp/kegg/) is our attempt to computerize current knowledge on various cellular processes as a collection of "generalized"protein-protein interaction networks, to develop new graph-based algorithms for predicting such networks from the genome information, and to actually reconstruct the interactomes for all the completely sequenced genomes and some partial genomes. During the reconstruction process, it becomes readily apparent that certain pathways and molecular complexes are present or absent in each organism, indicating modular structures of the interactome. In addition, the reconstruction uncovers missing components in an otherwise complete pathway or complex, which may result from misannotation of the genome or misrepresentation of the KEGG pathway. When combined with additional experimental data on protein-protein interactions, such as by yeast two-hybrid systems, the reconstruction possibly uncovers unknown partners for a particular pathway or complex. Thus, the reconstruction is tightly coupled with the annotation of individual genes, which is maintained in the GENES database in KEGG. We are also trying to expand our literature surrey to include in the GENES database most up-to-date information about gene functions.

• The Plant Pathology Journal
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• v.37 no.2
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• pp.152-161
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• 2021

Sugar beet (Beta vulgaris L.) is known as a key product for agriculture in several countries across the world. Beet soil-borne virus (BSBV) triggers substantial economic damages to sugar beet by reducing the quantity of the yield and quality of the beet sugars. We conducted the present study to report the complete genome sequences of two BSBV isolates in Turkey for the first time. The genome organization was identical to those previously established BSBV isolates. The tripartite genome of BSBV-TR1 and -TR3 comprised a 5,835-nucleotide (nt) RNA1, a 3,454-nt RNA2, and a 3,005-nt RNA3 segment. According to sequence identity analyses, Turkish isolates were most closely related to the BSBV isolate reported from Iran (97.83-98.77% nt identity). The BSBV isolates worldwide (n = 9) were phylogenetically classified into five (RNA-coat protein read through gene [CPRT], TGB1, and TGB2 segments), four (RNA-rep), or three (TGB3) lineages. In genetic analysis, the TGB3 revealed more genetic variability (Pi = 0.034) compared with other regions. Population selection analysis revealed that most of the codons were generally under negative selection or neutral evolution in the BSBV isolates studied. However, positive selection was detected at codon 135 in the TGB1, which could be an adaptation in order to facilitate the movement and overcome the host plant resistance genes. We expect that the information on genome properties and genetic variability of BSBV, particularly in TGB3, TGB1, and CPRT genes, assist in developing effective control measures in order to prevent severe losses and make amendments in management strategies.

• Journal of Forest and Environmental Science
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• v.28 no.4
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• pp.278-281
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• 2012

Comparative sequence analyses were conducted on complete mtDNA sequences from four small mammal species in Korea and revealed the presence of 30 well conserved sequences in various regions of the complete mtDNA sequences. The conserved sequences were found in 9 regions in protein coding genes, 10 regions in tRNA genes, 10 in rRNA genes, one region in replication origin and 2 regions in D loop. They could be used to design primers for amplifying complete mtDNA sequences of small mammals.

• Proceedings of the Korean Society for Applied Microbiology Conference
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• 2001.06a
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• pp.15-19
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• 2001

Creating an artificial strain with a minimal gene set for a specific purpose is every biologist's dream. With the complete genome sequencing of more than 50 microorganisms and extensive functional analyses of their genes, it is possible to design a genetic blueprint for a simple custom-designed microbe with the minimal gene set. Two different approaches are being considered. The first 'top-down' approach is trimming the genome to a minimal gene set by selectively removing genes of an organism thought to be unnecessary based on microbial genomics. The second 'bottom-up' approach is to synthesize the proposed minimal genome from basic chemical building blocks. The 'top-down' approach starting with the genome of a well known microorganism is more technically feasible, whereas the bottom-up approach may not be attainable in the nearest future because of the lack of the complete functional analysis of the genes needed for a life. Here in this study, we used the top-down approach to minimize the E. coli genome to create an artificial organism with 'core' elements for self-sustaining and self-replicating cells by eliminating unnecessary genes. Using several different kinds of sophisticated deletion techniques combined with a p:1age and transposons, we deleted about 19％ of the E. coli genome without causing any damages to cellular growth. This smaller E. coli genome will be further reduced to a genome with a minimal gene l;et essential for cell life. This minimized E. coli genome can lead to the construction of many custom-designed strains with myriad practical and commercial applications.

• Journal of Microbiology and Biotechnology
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• v.30 no.2
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• pp.237-243
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• 2020

A novel psychrotolerant Psychrobacillus strain PB01, isolated from an Antarctic iceberg, was comparatively analyzed with five related strains. The complete genome of strain PB01 consists of a single circular chromosome (4.3 Mb) and a plasmid (19 Kb). As potential low-temperature adaptation strategies, strain PB01 has four genes encoding cold-shock proteins, two genes encoding DEAD-box RNA helicases, and eight genes encoding transporters for glycine betaine, which can serve as a cryoprotectant, on the genome. The pan-genome structure of the six Psychrobacillus strains suggests that strain PB01 might have evolved to adapt to extreme environments by changing its genome content to gain higher capacity for DNA repair, translation, and membrane transport. Notably, strain PB01 possesses a complete TCA cycle consisting of eight enzymes as well as three additional Helicobacter pylori-type enzymes: ferredoxin-dependent 2-oxoglutarate synthase, succinyl-CoA/acetoacetyl-CoA transferase, and malate/quinone oxidoreductase. The co-existence of the genes for TCA cycle enzymes has also been identified in the other five Psychrobacillus strains.